Dear Sister Saadia,
Please give Sr. Saad benefit of doubt. I am sure she did not use or mean “mysteries” in a negative way. She might have meant to say “wonders”, i.e. Quran is full of wonders. Sometimes our Paki Brother/Sisters select wrong English word inadvertently. I often talked to my niece, who was a graduate student in Karachi majoring in English. During conversations as well as in her writings, she often chose wrong English words. Even very educated persons can make such mistakes.
Another possibility is that she might have meant the tafsirs. Doubtless, all tafsirs, especially, Tafsir Ibn Kathir and Syed Maududi’s Tafheem-Ul-Quran are full of mind boggling mysteries.